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SI for From Serological Surveys to Disease Burden: A Modelling Pipeline for Chagas Disease

This work is a collaboration between BioRISC (the Biosecurity Research Initiative at St Catharine’s College, Cambridge), Conservation Evidence based in the Department of Zoology, University of Cambridge and the Centre for the Study of Existential Risk. It was created by documenting our experience of options, consulting guidance, contacting people working in different countries to explore the range of options and crowd-sourcing ideas through social media. We welcome suggestions for options missed (especially those implemented outside of the UK), innovations for novel options or means of improving existing options. Please contact biorisc@caths.cam.ac.uk. You can also view the list of options on the BioRISC website (https://covid-19.biorisc.com/) or customise the list yourself using this app we developed (https://alecchristie888.shinyapps.io/Covid_19_options/).

Additional file 1.

Funder: Alborada Trust, The Covid-19 pandemic is of zoonotic origin, and many other emerging infections of humans have their origin in an animal host population. We review the challenges involved in modelling the dynamics of wildlife-human interfaces governing infectious disease emergence and spread. We argue that we need a better understanding of the dynamic nature of such interfaces, the underpinning diversity of pathogens and host-pathogen association networks, and the scales and frequencies at which environmental conditions enable spillover and host shifting from animals to humans to occur. The major drivers of the emergence of zoonoses are anthropogenic, including the global change in climate and land use. These, and other ecological processes pose challenges that must be overcome to counterbalance pandemic risk. The development of more detailed and nuanced models will provide better tools for analysing and understanding infectious disease emergence and spread.

First paragraph: In their Letter “Trophy hunting bans imperil biodiversity” (30 August, p.874), A. Dickman et al. warn that banning trophy hunting, a practice many of them deem “repugnant,” could threaten African biodiversity and livelihoods. What they actually describe is how loss of funding may impart these effects, without specifying any unique benefits of trophy hunting. It is defeatist to defend business-as-usual instead of promoting alternative conservation activities that could sustain formerly trophy-hunted species and areas.

Fire is a key driver in savannah systems and widely used as a land management tool. Intensifying human land uses are leading to rapid changes in the fire regimes, with consequences for ecosystem functioning and composition. We undertake a novel analysis describing spatial patterns in the fire regime of the Serengeti-Mara ecosystem, document multidecadal temporal changes, and investigate the factors underlying these patterns. We used MODIS active fire and burned area products from 2001-2014 to identify individual fires; summarising four characteristics for each detected fire: size, ignition date, time since last fire, and radiative power. Using satellite imagery, we estimated the rate of change in the density of livestock bomas as a proxy for livestock density. We used these metrics to model drivers of variation in the four fire characteristics, as well as total number of fires and total area burned. Fires in the Serengeti-Mara show high spatial variability - with number of fires and ignition date mirroring mean annual precipitation. The short term effect of rainfall decreases fire size and intensity but cumulative rainfall over several years leads to increased standing grass biomass and fuel loads, and therefore in larger and hotter fires. Our study reveals dramatic changes over time, with a reduction in total number of fires and total area burned. We suggest that increasing livestock numbers are driving this decline, presumably by inhibiting fire spread. Fire plays a crucial role in modulating spatial heterogeneity and in savannahs and some areas now experience virtually no fire. These temporal patterns are part of a global decline in total area burned, especially in savannahs, and we caution that healthy ecosystem functioning may have been compromised. Land managers and policy formulators need to factor in rapid fire regime modifications to achieve management objectives and maintain the integrity of savannah ecosystems

Conservation takes place within social–ecological systems, and many conservation interventions aim to influence human behaviour in order to push these systems towards sustainability. Predictive models of human behaviour are potentially powerful tools to support these interventions. This is particularly true if the models can link the attributes and behaviour of individuals with the dynamics of the social and environmental systems within which they operate. Here we explore this potential by showing how combining two modelling approaches (social network analysis, SNA, and agent-based modelling, ABM) could lead to more robust insights into a particular type of conservation intervention. We use our simple model, which simulates knowledge of ranger patrols through a hunting community and is based on empirical data from a Cambodian protected area, to highlight the complex, context-dependent nature of outcomes of information-sharing interventions, depending both on the configuration of the network and the attributes of the agents. We conclude by reflecting that both SNA and ABM, and many other modelling tools, are still too compartmentalized in application, either in ecology or social science, despite the strong methodological and conceptual parallels between their uses in different disciplines. Even a greater sharing of methods between disciplines is insufficient, however; given the impact of conservation on both the social and ecological aspects of systems (and vice versa), a fully integrated approach is needed, combining both the modelling approaches and the disciplinary insights of ecology and social science. This article is part of the theme issue ‘Linking behaviour to dynamics of populations and communities: application of novel approaches in behavioural ecology to conservation’.

Pathogen spillover from wildlife to domestic animals and humans, and the reverse, has caused significant epidemics and pandemics worldwide. Although pathogen emergence has been linked to anthropogenic land conversion, a general framework to disentangle underlying processes is lacking. We develop a multi-host model for pathogen transmission between species inhabiting intact and converted habitat. Interspecies contacts and host populations vary with the proportion of land converted; enabling us to quantify infection risk across a changing landscape. In a range of scenarios, the highest spillover risk occurs at intermediate levels of habitat loss, whereas the largest, but rarest, epidemics occur at extremes of land conversion. This framework provides insights into the mechanisms driving disease emergence and spillover during land conversion. The finding that the risk of spillover is highest at intermediate levels of habitat loss provides important guidance for conservation and public health policy.

This work provides compact representations for single- and multi-robot motion planning in the context of prehensile robot manipulation. This work describes the asymptotic near-optimality and probabilistic near-optimality properties of these planners. Probabilistic near-optimality is leveraged to provide practical and grounded stopping criteria for these methods which probabilistically guarantee the methods return high-quality paths. It is also shown how these methods can be leveraged to produce a compact planning representation, which is a lightweight structure that is quick to query and easy to store. The work also outlines a compact representation for solving multi-arm manipulation tasks, and integrates a scalable, asymptotically optimal multi-robot motion planning method to provide scalable, globally asymptotically optimal task and motion planning in manipulation domains.

Details of models

Lyme disease is the most common tick-borne disease in temperate regions of North America, Europe and Asia, and the number of reported cases has increased in many regions as landscapes have been altered. Although there has been extensive work on the ecology and epidemiology of this disease in both Europe and North America, substantial uncertainty exists about fundamental aspects that determine spatial and temporal variation in both disease risk and human incidence, which hamper effective and efficient prevention and control. Here we describe areas of consensus that can be built on, identify areas of uncertainty and outline research needed to fill these gaps to facilitate predictive models of disease risk and the development of novel disease control strategies. Key areas of uncertainty include: (i) the precise influence of deer abundance on tick abundance, (ii) how tick populations are regulated, (iii) assembly of host communities and tick-feeding patterns across different habitats and (iv) reservoir competence of host species and pathogenicity for humans of different genotypes of Borrelia burgdorferi. Filling these knowledge gaps will improve Lyme disease prevention and control and provide general insights into the drivers and dynamics of this emblematic multi-host–vector-borne zoonotic disease.This article is part of the themed issue ‘Conservation, biodiversity and infectious disease: scientific evidence and policy implications'.

This paper describes the design, tuning, and extensive field testing of an admittance-based Autonomous Loading Controller (ALC) for robotic excavation. Several iterations of the ALC were tuned and tested in fragmented rock piles—similar to those found in operating mines—by using both a robotic 1-tonne capacity Kubota R520S diesel-hydraulic surface loader and a 14-tonne capacity Atlas Copco ST14 underground load-haul-dump (LHD) machine. On the R520S loader, the ALC increased payload by 18 % with greater consistency, although with more energy expended and longer dig times when compared with digging at maximum actuator velocity. On the ST14 LHD, the ALC took 61 % less time to load 39 % more payload when compared to a single manual operator. The manual operator made 28 dig attempts by using three different digging strategies, and had one failed dig. The tuned ALC made 26 dig attempts at 10 and 11 MN target force levels. All 10 11 MN digs succeeded while 6 of the 16 10 MN digs failed. The results presented in this paper suggest that the admittance-based ALC is more productive and consistent than manual operators, but that care should be taken when detecting entry into the muck pile

Models used to investigate the relationship between biodiversity change and vector-borne disease risk often do not explicitly include the vector; they instead rely on a frequency-dependent transmission function to represent vector dynamics. However, differences between classes of vector (e.g., ticks and insects) can cause discrepancies in epidemiological responses to environmental change. Using a pair of disease models (mosquito- and tick-borne), we simulated substitutive and additive biodiversity change (where noncompetent hosts replaced or were added to competent hosts, respectively), while considering different relationships between vector and host densities. We found important differences between classes of vector, including an increased likelihood of amplified disease risk under additive biodiversity change in mosquito models, driven by higher vector biting rates. We also draw attention to more general phenomena, such as a negative relationship between initial infection prevalence in vectors and likelihood of dilution, and the potential for a rise in density of infected vectors to occur simultaneously with a decline in proportion of infected hosts. This has important implications; the density of infected vectors is the most valid metric for primarily zoonotic infections, while the proportion of infected hosts is more relevant for infections where humans are a primary host.

Parasitism is the most common consumer strategy among organisms, yet only recently has there been a call for the inclusion of infectious disease agents in food webs. The value of this effort hinges on whether parasites affect food-web properties. Increasing evidence suggests that parasites have the potential to uniquely alter food-web topology in terms of chain length, connectance and robustness. In addition, parasites might affect food-web stability, interaction strength and energy flow. Food-web structure also affects infectious disease dynamics because parasites depend on the ecological networks in which they live. Empirically, incorporating parasites into food webs is straightforward. We may start with existing food webs and add parasites as nodes, or we may try to build food webs around systems for which we already have a good understanding of infectious processes. In the future, perhaps researchers will add parasites while they construct food webs. Less clear is how food-web theory can accommodate parasites. This is a deep and central problem in theoretical biology and applied mathematics. For instance, is representing parasites with complex life cycles as a single node equivalent to representing other species with ontogenetic niche shifts as a single node? Can parasitism fit into fundamental frameworks such as the niche model? Can we integrate infectious disease models into the emerging field of dynamic food-web modelling? Future progress will benefit from interdisciplinary collaborations between ecologists and infectious disease biologists.

No abstract available.

Background Dengue virus (DENV) infection is prevalent across tropical regions and may cause severe disease. Early diagnosis may improve supportive care. We prospectively assessed the Standard Diagnostics (Korea) BIOLINE Dengue Duo DENV rapid diagnostic test (RDT) to NS1 antigen and anti-DENV IgM (NS1 and IgM) in children in Cambodia, with the aim of improving the diagnosis of DENV infection. Methodology and principal findings We enrolled children admitted to hospital with non-localised febrile illnesses during the 5-month DENV transmission season. Clinical and laboratory variables, and DENV RDT results were recorded at admission. Children had blood culture and serological and molecular tests for common local pathogens, including reference laboratory DENV NS1 antigen and IgM assays. 337 children were admitted with non-localised febrile illness over 5 months. 71 (21%) had DENV infection (reference assay positive). Sensitivity was 58%, and specificity 85% for RDT NS1 and IgM combined. Conditional inference framework analysis showed the additional value of platelet and white cell counts for diagnosis of DENV infection. Variables associated with diagnosis of DENV infection were not associated with critical care admission (70 children, 21%) or mortality (19 children, 6%). Known causes of mortality were melioidosis (4), other sepsis (5), and malignancy (1). 22 (27%) children with a positive DENV RDT had a treatable other infection. Conclusions The DENV RDT had low sensitivity for the diagnosis of DENV infection. The high co-prevalence of infections in our cohort indicates the need for a broad microbiological assessment of non-localised febrile illness in these children., Author Summary DENV infection first manifests as an undifferentiated fever before either settling without complications, or progressing to severe disease requiring inpatient admission and careful supportive intravenous fluid management. The ability to differentiate DENV infection from other febrile illnesses, and to predict those at risk of severe disease is likely to be important. We assessed the diagnostic accuracy of a commercially available DENV rapid diagnostic test (RDT) for children admitted with febrile illness to a hospital in Cambodia during the DENV transmission season. We found sensitivity of the DENV RDT to be 58% and specificity to be 85% versus reference assay DENV serology. We then modelled the ability of clinical features, basic laboratory parameters, and DENV RDT result at presentation of the child to distinguish DENV infection from other febrile illness, and determine the need for critical care admission. We found that the DENV RDT did not increase the accuracy with which we diagnosed DENV infection, and was not helpful in deciding which children required critical care admission. Indeed, the relatively high prevalence of serious bacterial disease in the cohort of children indicated a broad microbiological differential diagnosis in all febrile children, regardless of their DENV infection status.

Non-invasive surveys for primate malarias. Raw data from studies that quantified Plasmodium detection from non-invasive samples.

Optimal storage techniques. Data on DNA yield from faecal samples stored with four different protocols that varied in temperature and media.

Forsøksresultatene som presenteres i denne rapporten er biologisk godkjenningsprøving av soppmidler utført på oppdrag fra Mattilsynet i 2014. Inkludert i rapporten er også forsøk eller egne forsøksledd som grupperes som biologisk utviklingsprøving. Forsøkene er utført etter GEP-kvalitet1 hvis ikke annet er nevnt. Dette innebærer at det er utarbeidet skriftlige prosedyrer for nesten alle arbeidsprosesser. Disse prosedyrene, kalt standardforskrifter (SF’er), er samlet i en kvalitetshåndbok. Denne er delt ut til alle personer som arbeider med utprøving av plantevernmidler. De samme personene har også vært med på et endagskurs i GEP-arbeid.

Citizenship, as a concept, is about the rights and duties of individuals (usually) in a given political territory (e.g., the state). In its participatory guises, it is normally associated with activity in the public sphere, and it may or not entail the cultivation and exercise of certain virtues. It is the specific design of this general architecture that gives us what we might call «adjectival citizenships» -e.g., liberal citizenship, republican citizenship, cosmopolitan citizenship-. Each of these types of citizenship interprets the architecture in different ways. So liberal citizenship tends to focus more on rights than on duties, republican citizenship speaks in the language of duty and of virtue, and cosmopolitan citizenship calls into question the territorial underpinnings of both these types of citizenship. This article explores the way in which ecological citizenship fills out the architecture of citizenship, before outlining the importance of ecological citizenship to the project of achieving sustainable development.La ciudadanía, como concepto, trata de los derechos y los deberes de los individuos (normalmente), y en un territorio político determinado (por ejemplo, un Estado). Bajo su vertiente participativa, la ciudadanía está normalmente asociada con la esfera pública, y puede suponer o no el cultivo y ejercicio de ciertas virtudes. El diseño específico de la arquitectura general del concepto de ciudadanía nos define lo que podríamos llamar «ciudadanías adjetivas» -por ejemplo, la ciudadanía liberal, la ciudadanía republicana o la ciudadanía cosmopolita-. Cada uno de estos tipos de ciudadanía interpreta la arquitectura de diferente manera. Así, la ciudadanía liberal tiende a centrarse más en los derechos que en los deberes, la ciudadanía republicana habla en el lenguaje del deber y la virtud, y la ciudadanía cosmopolita cuestiona los argumentos territoriales de los otros dos tipos de ciudadanía. Este artículo explora el modo en que la ciudadanía ecológica completa la arquitectura general de la ciudadanía, antes de perfilar la importancia de la ciudadanía ecológica para el objetivo de lograr el desarrollo sostenible.

Sampling-based motion planners have proven to be efficient solutions to a variety of high-dimensional, geometrically complex motion planning problems with applications in several domains. The traditional view of these approaches is that they solve challenges efficiently by giving up formal guarantees and instead attain asymptotic properties in terms of completeness and optimality. Recent work has argued based on Monte Carlo experiments that these approaches also exhibit desirable probabilistic properties in terms of completeness and optimality after finite computation. The current paper formalizes these guarantees. It proves a formal bound on the probability that solutions returned by asymptotically optimal roadmap-based methods (e.g., PRM*) are within a bound of the optimal path length I* with clearance {\epsilon} after a finite iteration n. This bound has the form P(|In - I* | {\leq} {\delta}I*) {\leq} Psuccess, where {\delta} is an error term for the length a path in the PRM* graph, In. This bound is proven for general dimension Euclidean spaces and evaluated in simulation. A discussion on how this bound can be used in practice, as well as bounds for sparse roadmaps are also provided., Comment: 17 pages, 5 figures, 3 tables. Submitted to the Eleventh International Workshop on the Algorithmic Foundations of Robotics (WAFR 2014)

This paper challenges “Big Society (BS) Localism”, seeing it as an example of impoverished localist thinking which neglects social justice considerations. We do this through a critical examination of recent turns in the localist discourse in the UK which emphasise self-reliant communities and envisage a diminished role for the state. We establish a heuristic distinction between positive and negative approaches to localism. We argue that the Coalition Government's BS programme fits with a negative localist frame as it starts from an ideological assumption that the state acts as a barrier to community-level associational activity and that it should play a minimal role. “BS localism” (as we call it) has been influential over the making of social policy, but it also has implications for the achievement of environmental goals. We argue that this latest incarnation of localism is largely ineffective in solving problems requiring collective action because it neglects the important role that inequalities play in inhibiting the development of associational society. Drawing upon preliminary research being undertaken at the community scale, we argue that staking environmental policy success on the ability of local civil society to fill the gap left after state retrenchment runs the risk of no activity at all.

BACKGROUND The risk posed by ticks as vectors of disease is typically assessed by blanket-drag sampling of host-seeking individuals. Comparisons of peak abundance between plots - either in order to establish their relative risk or to identify environmental correlates - are often carried out by sampling on one or two occasions during the period of assumed peak tick activity. METHODS This paper simulates this practice by 're-sampling' from model datasets derived from an empirical field study. Re-sample dates for each plot are guided by either the previous year's peak at the plot, or the previous year's peak at a similar, nearby plot. Results from single, double and three-weekly sampling regimes are compared. RESULTS Sampling on single dates within a two-month window of assumed peak activity has the potential to introduce profound errors; sampling on two dates (double sampling) offers greater precision, but three-weekly sampling is the least biased. CONCLUSIONS The common practice of sampling for the abundance of host-seeking ticks on single dates in each plot-year should be strenuously avoided; it is recommended that field acarologists employ regular sampling throughout the year at intervals no greater than three weeks, for a variety of epidemiological studies.

Forsøksresultatene som presenteres i denne rapporten er biologisk godkjenningsprøving av soppmidler utført på oppdrag fra Mattilsynet i 2012. Inkludert i rapporten er også forsøk eller egne forsøksledd som grupperes som biologisk utviklingsprøving. Forsøkene er utført etter GEP-kvalitet1 hvis ikke annet er nevnt. Dette innebærer at det er utarbeidet skriftlige prosedyrer for nesten alle arbeidsprosesser. Disse prosedyrene, kalt standardforskrifter (SF’er), er samlet i en kvalitetshåndbok. Denne er delt ut til alle personer som arbeider med utprøving av plantevernmidler. De samme personene har også vært med på et endagskurs i GEP-arbeid.

The twin concepts of zooprophylaxis and the dilution effect originated with vector-borne diseases (malaria), were driven forward by studies on Lyme borreliosis and have now developed into the mantra "biodiversity protects against disease". The basic idea is that by diluting the assemblage of transmission-competent hosts with non-competent hosts, the probability of vectors feeding on transmission-competent hosts is reduced and so the abundance of infected vectors is lowered. The same principle has recently been applied to other infectious disease systems - tick-borne, insect-borne, indirectly transmitted via intermediate hosts, directly transmitted. It is claimed that the presence of extra species of various sorts, acting through a variety of distinct mechanisms, causes the prevalence of infectious agents to decrease. Examination of the theoretical and empirical evidence for this hypothesis reveals that it applies only in certain circumstances even amongst tick-borne diseases, and even less often if considering the correct metric - abundance rather than prevalence of infected vectors. Whether dilution or amplification occurs depends more on specific community composition than on biodiversity per se. We warn against raising a straw man, an untenable argument easily dismantled and dismissed. The intrinsic value of protecting biodiversity and ecosystem function outweighs this questionable utilitarian justification.

Capsule: The majority of Hen Harriers Circus cyaneus that spend the winter in England are derived from the British breeding population. Aims: To investigate the popular hypothesis that Hen Harriers which over-winter in England are derived principally from breeding populations in mainland Europe. Methods: Demographic data were used to estimate numbers of Hen Harriers in Britain at the end of the breeding season. This figure was used, together with data from winter (October-March inclusive) recoveries of Hen Harriers ringed in Britain during the breeding season, to estimate the number of birds from the British breeding population wintering in England and in other parts of Europe. Results: It was estimated that Hen Harriers wintering in England are derived primarily from British breeding populations. Published winter population figures for British Hen Harriers may be significant underestimates. Conclusion: The link between breeding and wintering populations of Hen Harriers in Britain is closer than previously thought. Conservation action should be spread more equally between the environmental factors which limit populations in different seasons. The winter population in Britain, as monitored by the Hen Harrier Winter Roost Survey, may provide a good indication of the status of the breeding population.

1. A population model for the tick Ixodes ricinus, the most significant vector of pathogens in Europe, is used to explore the relative impact of changes in climate, host density and acaricide-treated hosts on tick abundance and seasonality. 2. A rise in temperature of the sort witnessed since 1989 speeds up the inter-stadial development of ticks, thereby reducing the cumulative effect of constant daily mortality rates and potentially raising population levels. The predicted earlier onset of tick-questing activity in the spring, due to stage-specific temperature thresholds, could increase contact between ticks and humans during recreational visits to the countryside in spring holidays. These tick population effects vary geographically with background climate. 3. The significant increase in deer abundance across Europe, including the UK, in recent decades is predicted to drive tick population increases, the effect varying with the initial density of hosts. In areas only recently colonized by deer, tick numbers are predicted to rise dramatically (given suitable climatic conditions). Where host densities are already high, however, further increases may reduce numbers of questing ticks; unfed ticks leave the questing population more rapidly, even though the overall tick population (and therefore pathogen transmission potential) increases. 4. Culling high-density deer populations as a control measure could, therefore, initially cause an apparent increase in questing ticks, with the predicted long-term population trajectory depending on the severity of the cull. 5. Conversely, the further addition of large hosts (e.g. sheep) would effectively reduce the number of questing ticks and therefore the risk to humans. If such sheep were treated with acaricide, tick populations are predicted to decrease rapidly, to an extent that depends on the relative abundance of wild (untreated) and treated hosts. Tick control in designated areas may be achieved by using sheep in this way as ‘lethal mops', as used to occur in the past when sheep were regularly dipped. 6.Synthesis and applications. Both abiotic and biotic environmental changes witnessed recently could have contributed to apparent increases in tick populations, especially where these environmental factors were limiting in the past. The release of additional hosts treated with long-lasting acaricide is potentially an effective control strategy.

Capsule: At a communal roost in Cambridgeshire, selection of common birds of arable farmland as prey is interpreted in terms of differences in prey species' behaviour and size.

The north-east Atlantic margin (NEAM) is important for hydrocarbon exploration because of the growing evidence of hydrocarbon reserves in the region. However, seismic exploration of the sub-surface is hampered by large deposits of flood basalts, which cover possible hydrocarbon-bearing reservoirs underneath. There are several hypotheses as to why imaging beneath basalt is a problem. These include: the high impedance contrast between the basalt and the layers above; the thin-layering of the basalt due to the many flows which make up a basalt succession; and the rough interfaces on the top-basalt interface caused by weathering and emplacement mechanisms. I perform forward modelling to assess the relative importance of these factors for imaging of sub-basalt reflections. The boundary element method (BEM) is used for the rough-interface modelling. The method was selected because only the interfaces between layers need to be discretized, in contrast to grid methods such as finite difference for which the whole model needs to be discretized, and so should lead to fast generation of shot gathers for models which have only a few homogeneous layers. I have had to develop criteria for accurate modelling with the boundary element method and have considered the following: source near an interface, two interfaces close together, removal of model edge effects and precise modelling of a transparent interface. I have improved efficiency of my code by: resampling the model so that fewer discretization elements are required at low frequencies, and suppressing wrap-around so that the time window length can be reduced. I introduce a new scheme which combines domain decomposition and a far-field approximation to improve the efficiency of the boundary element code further. I compare performance with a standard finite difference code. I show that the BEM is well suited to seismic modelling in an exploration environment when there are only a few layers in the model and when a seismic profile containing many shot gathers for one model is required. For many other cases the finite difference code is still the best option. The input models for the forward modelling are based on real seismic data which were acquired in the Faeroe-Shetland Channel in 2001. The modelling shows that roughness on the surface of the basalt has little effect on the imaging in this particular area of the NEAM. The thin layers in the basalt act as a low-pass filter to the seismic wave. For the real-data acquisition, even the topbasalt reflection is a low frequency event. This is most likely to be due to high attenuation in the layers above the basalt. I show that sea-surface multiple energy is considerable and that it could mask possible sub-basalt events on a seismic shot gather, but any shallow sub-basalt events should still be visible even with the presence of multiple energy. This leaves the possibility that there is only one major stratigraphic unit between the base of the basalt and the crystalline basement. The implication of the forward modelling and real data analysis for acquisition is that the acquisition parameters must emphasize the low frequencies, since the high frequencies are attenuated before they even reach the top-basalt interface. The implication for processing is that multiple removal is of prime importance.

The goal of fisheries assessment is to predict the consequences of fishing and other environmental interventions and, on that basis, evaluate how different management schemes fare at achieving various management goals. Forecasting the state and harvest of exploited populations and communities is thus central to fishery science.There are two broad approaches that can be used to forecast fisheries population and harvest. On the one hand, there are short-term forecasts aimed at predicting the size of the exploitable stock for the upcoming fishing season in order to implement a predetermined feedback harvest rule. In this case, the forecast is part of the tactic used to define regulatory measures for the fishing season, such as the total allowable catch or the number of allowable effort units. This type of forecast is critical for fisheries based on shortlived or semelparous species (species that reproduce once and then die), where the bulk or all of the annual catch is made up of new recruits.Mid- and long-term forecasts of populations, on the other hand, are used in policy design to examine likely consequences of different management options and thus guide strategic decision-making. In contrast to short-term tactical forecasts, mid- and long-term forecasts are not meant to actually predict the future of the system under exploitation; rather, they attempt to represent a full range of scenarios that are deemed possible based on historical experience. Because our ability to actually predict the responses of natural systems to harvest is admittedly limited, the emphasis in policy design is on feedback and robustness of performance across scenarios. Mid- and long-term forecasts aimed at guiding general management approaches are difficult because they require more information than the most recent harvest rates and data on catch per unit of effort, but it is not clear which of many possible auxiliary data will be most useful or how much history to consider. Fil: Agard, John B. R.. No especifíca; Fil: Alder, Jacqueline. No especifíca; Fil: Bennett, Elena. No especifíca; Fil: Butler, Colin. No especifíca; Fil: Carpenter, Steve. No especifíca; Fil: Cheung, W. W. L.. No especifíca; Fil: Cumming, Graeme S.. No especifíca; Fil: Defries, Ruth. No especifíca; Fil: de Vries, Bert. No especifíca; Fil: Dickinson, Robert E.. No especifíca; Fil: Dobson, Andrew. No especifíca; Fil: Foley, Jonathan A.. No especifíca; Fil: Geoghegan, Jacqueline. No especifíca; Fil: Holland, Beth. No especifíca; Fil: Kabat, Pavel. No especifíca; Fil: Keymer, Juan. No especifíca; Fil: Kleidon, Axel. No especifíca; Fil: Lodge, David. No especifíca; Fil: Manson, Steven M.. No especifíca; Fil: McGlade, Jacquie. No especifíca; Fil: Mooney, Hal. No especifíca; Fil: Parma, Ana María. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; Argentina Fil: Pascual, Miguel Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; Argentina Fil: Pereira, Henrique M.. No especifíca; Fil: Rosegrant, Mark. No especifíca; Fil: Ringler, Claudia. No especifíca; Fil: Sala, Osvaldo Esteban. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Turner II,B. L.. No especifíca; Fil: van Vuuren, Detlef. No especifíca; Fil: Wall, Diana H.. No especifíca; Fil: Wilkinson, Paul. No especifíca; Fil: Wolters, Volkmar. No especifíca

© 2014 The Authors. Many disease systems exhibit complexities not captured by current theoretical and empirical work. In particular, systems with multiple host species and multiple infectious agents (i.e., multi-host, multi-agent systems) require novel methods to extend the wealth of knowledge acquired studying primarily single-host, single-agent systems. We outline eight challenges in multi-host, multi-agent systems that could substantively increase our knowledge of the drivers and broader ecosystem effects of infectious disease dynamics.

Lyme disease is the most common tick-borne disease in temperate regions of North America, Europe and Asia, and the number of reported cases has increased in many regions as landscapes have been altered. Although there has been extensive work on the ecology and epidemiology of this disease in both Europe and North America, substantial uncertainty exists about fundamental aspects that determine spatial and temporal variation in both disease risk and human incidence, which hamper effective and efficient prevention and control. Here we describe areas of consensus that can be built on, identify areas of uncertainty and outline research needed to fill these gaps to facilitate predictive models of disease risk and the development of novel disease control strategies. Key areas of uncertainty include: (i) the precise influence of deer abundance on tick abundance, (ii) how tick populations are regulated, (iii) assembly of host communities and tick-feeding patterns across different habitats and (iv) reservoir competence of host species and pathogenicity for humans of different genotypes of Borrelia burgdorferi. Filling these knowledge gaps will improve Lyme disease prevention and control and provide general insights into the drivers and dynamics of this emblematic multi-host–vector-borne zoonotic disease.This article is part of the themed issue ‘Conservation, biodiversity and infectious disease: scientific evidence and policy implications'.

Lyme disease is the most common tick-borne disease in temperate regions of North America, Europe and Asia, and the number of reported cases has increased in many regions as landscapes have been altered. Although there has been extensive work on the ecology and epidemiology of this disease in both Europe and North America, substantial uncertainty exists about fundamental aspects that determine spatial and temporal variation in both disease risk and human incidence, which hamper effective and efficient prevention and control. Here we describe areas of consensus that can be built on, identify areas of uncertainty and outline research needed to fill these gaps to facilitate predictive models of disease risk and the development of novel disease control strategies. Key areas of uncertainty include: (i) the precise influence of deer abundance on tick abundance, (ii) how tick populations are regulated, (iii) assembly of host communities and tick-feeding patterns across different habitats and (iv) reservoir competence of host species and pathogenicity for humans of different genotypes of Borrelia burgdorferi. Filling these knowledge gaps will improve Lyme disease prevention and control and provide general insights into the drivers and dynamics of this emblematic multi-host–vector-borne zoonotic disease.This article is part of the themed issue ‘Conservation, biodiversity and infectious disease: scientific evidence and policy implications'.

Conservation takes place within social–ecological systems, and many conservation interventions aim to influence human behaviour in order to push these systems towards sustainability. Predictive models of human behaviour are potentially powerful tools to support these interventions. This is particularly true if the models can link the attributes and behaviour of individuals with the dynamics of the social and environmental systems within which they operate. Here we explore this potential by showing how combining two modelling approaches (social network analysis, SNA, and agent-based modelling, ABM) could lead to more robust insights into a particular type of conservation intervention. We use our simple model, which simulates knowledge of ranger patrols through a hunting community and is based on empirical data from a Cambodian protected area, to highlight the complex, context-dependent nature of outcomes of information-sharing interventions, depending both on the configuration of the network and the attributes of the agents. We conclude by reflecting that both SNA and ABM, and many other modelling tools, are still too compartmentalized in application, either in ecology or social science, despite the strong methodological and conceptual parallels between their uses in different disciplines. Even a greater sharing of methods between disciplines is insufficient, however; given the impact of conservation on both the social and ecological aspects of systems (and vice versa), a fully integrated approach is needed, combining both the modelling approaches and the disciplinary insights of ecology and social science.This article is part of the theme issue ‘Linking behaviour to dynamics of populations and communities: application of novel approaches in behavioural ecology to conservation’.

Lyme disease is the most common tick-borne disease in temperate regions of North America, Europe and Asia, and the number of reported cases has increased in many regions as landscapes have been altered. Although there has been extensive work on the ecology and epidemiology of this disease in both Europe and North America, substantial uncertainty exists about fundamental aspects that determine spatial and temporal variation in both disease risk and human incidence, which hamper effective and efficient prevention and control. Here we describe areas of consensus that can be built on, identify areas of uncertainty and outline research needed to fill these gaps to facilitate predictive models of disease risk and the development of novel disease control strategies. Key areas of uncertainty include: (i) the precise influence of deer abundance on tick abundance, (ii) how tick populations are regulated, (iii) assembly of host communities and tick-feeding patterns across different habitats and (iv) reservoir competence of host species and pathogenicity for humans of different genotypes of Borrelia burgdorferi. Filling these knowledge gaps will improve Lyme disease prevention and control and provide general insights into the drivers and dynamics of this emblematic multi-host–vector-borne zoonotic disease.This article is part of the themed issue ‘Conservation, biodiversity and infectious disease: scientific evidence and policy implications'.

Conservation takes place within social–ecological systems, and many conservation interventions aim to influence human behaviour in order to push these systems towards sustainability. Predictive models of human behaviour are potentially powerful tools to support these interventions. This is particularly true if the models can link the attributes and behaviour of individuals with the dynamics of the social and environmental systems within which they operate. Here we explore this potential by showing how combining two modelling approaches (social network analysis, SNA, and agent-based modelling, ABM) could lead to more robust insights into a particular type of conservation intervention. We use our simple model, which simulates knowledge of ranger patrols through a hunting community and is based on empirical data from a Cambodian protected area, to highlight the complex, context-dependent nature of outcomes of information-sharing interventions, depending both on the configuration of the network and the attributes of the agents. We conclude by reflecting that both SNA and ABM, and many other modelling tools, are still too compartmentalized in application, either in ecology or social science, despite the strong methodological and conceptual parallels between their uses in different disciplines. Even a greater sharing of methods between disciplines is insufficient, however; given the impact of conservation on both the social and ecological aspects of systems (and vice versa), a fully integrated approach is needed, combining both the modelling approaches and the disciplinary insights of ecology and social science.This article is part of the theme issue ‘Linking behaviour to dynamics of populations and communities: application of novel approaches in behavioural ecology to conservation’.

Bats are reservoirs for emerging human pathogens, including Hendra and Nipah henipaviruses and Ebola and Marburg filoviruses. These viruses demonstrate predictable patterns in seasonality and age structure across multiple systems; previous work suggests that they may circulate in Madagascar's endemic fruit bats, which are widely consumed as human food. We aimed to (a) document the extent of henipa- and filovirus exposure among Malagasy fruit bats, (b) explore seasonality in seroprevalence and serostatus in these bat populations and (c) compare mechanistic hypotheses for possible transmission dynamics underlying these data. To this end, we amassed and analysed a unique dataset documenting longitudinal serological henipa- and filovirus dynamics in three Madagascar fruit bat species. We uncovered serological evidence of exposure to Hendra-/Nipah-related henipaviruses in Eidolon dupreanum, Pteropus rufus and Rousettus madagascariensis, to Cedar-related henipaviruses in E. dupreanum and R. madagascariensis and to Ebola-related filoviruses in P. rufus and R. madagascariensis. We demonstrated significant seasonality in population-level seroprevalence and individual serostatus for multiple viruses across these species, linked to the female reproductive calendar. An age-structured subset of the data highlighted evidence of waning maternal antibodies in neonates, increasing seroprevalence in young and decreasing seroprevalence late in life. Comparison of mechanistic epidemiological models fit to these data offered support for transmission hypotheses permitting waning antibodies but retained immunity in adult-age bats. Our findings suggest that bats may seasonally modulate mechanisms of pathogen control, with consequences for population-level transmission. Additionally, we narrow the field of candidate transmission hypotheses by which bats are presumed to host and transmit potentially zoonotic viruses globally.

International audience; Bats are reservoirs for emerging human pathogens, including Hendra and Nipah henipaviruses and Ebola and Marburg filoviruses. These viruses demonstrate predictable patterns in seasonality and age structure across multiple systems; previous work suggests that they may circulate in Madagascar's endemic fruit bats, which are widely consumed as human food. We aimed to (a) document the extent of henipa- and filovirus exposure among Malagasy fruit bats, (b) explore seasonality in seroprevalence and serostatus in these bat populations and (c) compare mechanistic hypotheses for possible transmission dynamics underlying these data. To this end, we amassed and analysed a unique dataset documenting longitudinal serological henipa- and filovirus dynamics in three Madagascar fruit bat species. We uncovered serological evidence of exposure to Hendra-/Nipah-related henipaviruses in Eidolon dupreanum, Pteropus rufus and Rousettus madagascariensis, to Cedar-related henipaviruses in E. dupreanum and R. madagascariensis and to Ebola-related filoviruses in P. rufus and R. madagascariensis. We demonstrated significant seasonality in population-level seroprevalence and individual serostatus for multiple viruses across these species, linked to the female reproductive calendar. An age-structured subset of the data highlighted evidence of waning maternal antibodies in neonates, increasing seroprevalence in young and decreasing seroprevalence late in life. Comparison of mechanistic epidemiological models fit to these data offered support for transmission hypotheses permitting waning antibodies but retained immunity in adult-age bats. Our findings suggest that bats may seasonally modulate mechanisms of pathogen control, with consequences for population-level transmission. Additionally, we narrow the field of candidate transmission hypotheses by which bats are presumed to host and transmit potentially zoonotic viruses globally.

Given the limitations of current governmental approaches in influencing people to take pro-environmental action, especially in the longer term, this thesis explores whether a shared morality towards nature can be developed. Focusing on one community in the UK, the thesis investigates the potential of this alternative approach, the means by which it can be developed and implemented, and its effectiveness. Through an exercise in practical philosophy which uses a variety of methods (a focus group, a questionnaire, multiple interviews, and a debriefing session), the research finds considerable public appetite for such an approach, and works with participants to first construct and then deploy a ‘moral code’ for environmental protection. The development and implementation of the approach prove effective amongst both ‘green’ and ‘non-green’ participants. It raises people’s awareness of the consequences of their unsustainable actions and motivates them to be more environmentally conscious. It also brings wider, collective benefits such as community well-being and mutual support. These findings indicate that a shared morality strategy to fostering respect for nature has significant potential. It could be rolled out in other settings and could usefully inform future policy-making aimed at environmental protection as well as wider active models of citizenship.

Ecologism is a political ideology that emerged in the 1970s. It challenged the neoliberal privileging of economic growth over environmental protection and a narrow conception of the self as autonomous, rational and self-interested. Ecologism’s normative challenge has grown quiet as it became perceived as too inward looking and focused on the self, rather than engaged with issues such as climate change that now preoccupy green political thought. However, in the early 21st century, neoliberalism now dominates western democracies. This turn away from the self and normative opposition to neoliberalism has clearly not furthered the environmental cause, and so there is a need to return to re-politicise the ontological arguments of ecologism.\ud \ud A small number of green political theorists have begun to look towards the Thomistic Aristotelianism of Alasdair MacIntyre and this thesis seeks to add to their number. I argue that MacIntyre’s work concerning the self as dependent rational animal, and arguments for the political and social structures that support this self, can be used to affirm and reengage ecological arguments with politics. MacIntyre’s thought moves ecologism away from its “inward-turn”, concerned with the self’s personal experience of the environment, to a collective politics that looks outwardly to challenge the dominant neoliberal order.\ud \ud In bringing ecologism into conversation with MacIntyre’s philosophy, the original contribution I offer ecological political theory is two-fold. Firstly, the virtues of acknowledged dependence can be used to reflect substantive concern for the environment within political deliberation. Secondly, I develop MacIntyre’s conception of localized deliberative democracy. In order to counter claims that such localization is naïve, I bring MacIntyre’s ideal into conversation with Murray Bookchin’s model of municipal libertarianism and consider two real world examples: Rojava in northern Syria and the ‘Idle no More movement’ in Canada. These examples offer hopeful evidence that decentralised deliberative politics, starting from acknowledging our dependence, can oppose the hegemony of neoliberalism both socially and ecologically.

This thesis argues from a non-ecocentric perspective that environmental policy should be underpinned by a strong conception of ecological sustainability, and should eschew liberal neutrality in favour of government based on a substantive conception of human flourishing which accepts and celebrates our ecological embeddedness. A relational understanding of autonomy shows that such policy need not conflict with the protection of freedom, and is hence potentially compatible with a perfectionist liberalism which aims at intergenerational justice of capabilities. However reflection on the ecologically unsustainable resource consumption levels typical of affluent capitalist economies suggests that while a capabilities framework (potentially including protection of some capabilities as environmental rights) may be effective in establishing 'floors' at the lower end of the range of ethically acceptable consumption levels, 'ceilings' at the top end are better justified by reference to a eudaimonist ecological virtue ethics which understands and promotes ecological virtue as a matter of enlightened self-interest. Appeals to ecological virtue are entirely congruent with a capabilities approach to sustainability. Exhortations to ecological virtue aimed at individuals by governments are nonetheless illegitimate unless accompanied by policies which embody as well as facilitate such virtue, and aim to remove incentives to ecological vice. This includes robust regulation of consumption drivers and restriction of unsustainable options. Objections to such policies appealing to 'freedom of choice' are ill-founded to the extent that they neglect to examine the value of the options chosen between.

About the book: This edited volume presents a unique challenge to mainstream political theory • Offers fourteen ‘think pieces’ by renowed international scholars • Presents a comprehensive examination of core political ideologies and core political concepts